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Plant Molecular Biology

, Volume 86, Issue 1–2, pp 85–92 | Cite as

Transcriptome comparison reveals the patterns of selection in domesticated and wild ramie (Boehmeria nivea L. Gaud)

  • Touming LiuEmail author
  • Shouwei Tang
  • Siyuan Zhu
  • Qingming Tang
  • Xia Zheng
Article

Abstract

Ramie is an old fiber crop, cultivated for thousands of years in China. The cultivar ramie evolved from the wild species Qingyezhuma (QYZM, Boehmeria nivea var. tenacissima). However, the mechanism of domestication of this old fiber crop is poorly understood. In order to characterize the selective pattern in ramie domestication, orthologous genes between the transcriptomes of domesticated ramie variety Zhongzhu 1 (ZZ1) and wild QYZM were assessed using bidirectional best-hit method and ratio of non-synonymous (Ka) to synonymous (Ks) nucleotide substitutions was estimated. Sequence comparison of 56,932 and 59,246 unigenes from the wild QYZM and domesticated ZZ1, respectively, helped identify 10,745 orthologous unigene pairs with a total orthologous length of 10.18 Mb. Among these unigenes, 85 and 13 genes were found to undergo significant purifying and positive selection, respectively. Most of the selected genes were homologs of those involved in abiotic stress tolerance or disease resistance in other plants, suggesting that abiotic and biotic stresses were important selective pressures in ramie domestication. Two genes probably related to the fiber yield of ramie were subjected to positive selection, which may be caused by human manipulation. Thus, our results show the pervasive effects of artificial and natural selections on the accelerated domestication of ramie from its wild relative.

Keywords

Ramie Transcriptome Ka/Ks Domestication Selective pattern 

Notes

Acknowledgments

We acknowledge the Novogene Bioinformatics Institute for its assistance in original data processing and related bioinformatics analysis. This work was supported by grants from the National Natural Science Foundation of China (31101189) and National Modern Agro-industry Technology Research System (nycytx-19-E16).

Supplementary material

11103_2014_214_MOESM1_ESM.doc (227 kb)
Figure S1 The 5′ and 3′ UTR length distribution of ZZ1 and QYZM unigenes (DOC 227 kb)
11103_2014_214_MOESM2_ESM.doc (282 kb)
Figure S2 The unigene number annotated in seven public databases searched (DOC 282 kb)
11103_2014_214_MOESM3_ESM.doc (915 kb)
Figure S3 Histogram presentation of eukaryotic Ortholog Groups (KOG) classification (DOC 915 kb)
11103_2014_214_MOESM4_ESM.xls (34 kb)
Table S1 Genes subjected to purifying selection in ramie domestication (XLS 33 kb)

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Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Touming Liu
    • 1
    Email author
  • Shouwei Tang
    • 1
  • Siyuan Zhu
    • 1
  • Qingming Tang
    • 1
  • Xia Zheng
    • 1
  1. 1.Institute of Bast Fiber CropsChinese Academy of Agricultural SciencesChangshaChina

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